When I rub my finger over mine I can feel it is is slightly raised out of the glass, but the button works perfectly. When you look at the iPad side-on you can just about see its like a hair width higher than the glass, I'm still happy with it though - it's not enough to notice unless you're looking for it. but if you find yours uncomfortable or unsightly then I feel you should have every right to replace it, Apple market themselves as the pinnacle of quality, and as such you expect this quality from them.
Much like I wouldn't buy an Audi and just live with a radio that was protruding form the center console. But if I bought a Diatsu that probably wouldent bother me.